KnetFold Homepage : RNA secondary structure prediction
Link to Homepage of Computational RNA structure group

KNetFold Homepage!

RNA secondary structure prediction based on machine learning


KNetFold is a software for predicting the consensus RNA secondary structure for a given alignment of nucleotide sequences. You can read about the scientific background of this software in the help document or in our recent publication: Bindewald, E and Shapiro B.A (2006): RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers. RNA. 12(3): 342-352 (2006).

The CyloFold web server is an option for analyzing single RNA sequences. For analyzing alignments of RNA sequences you also might want to try our 3D sequence logo generator called CorreLogo .
This server was developed in the research group of Dr. Bruce A. Shapiro. This server is hosted by the Advanced Biomedical Computing Center (ABCC) of the National Cancer Institute (Frederick Campus).

Quick start

For a really quick start, simply use the form filled with the example tRNA alignment and click "submit". If you want to compute a prediction using your own set of sequences, you need to paste a set aligned RNA sequences (in FASTA format) into the sequence text area of the form below. Providing the email address is currently not possible. To retrieve the results, please store the job id that is shown on the screen after job submission, because computing the results can take more than an hour (depending on the length of the submitted alignment). The use of the options is explained in the help text. To obtain old results go to the result retriever page.



Fill text area with example sequences tRNA, tRNA anticodon loop

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Reference:

Bindewald, E and Shapiro B.A (2006): RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers. RNA. 12(3): 342-352 (2006).